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- PDB-2bd7: Porcine pancreatic elastase complexed with beta-casomorphin-7 and... -

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Basic information

Entry
Database: PDB / ID: 2bd7
TitlePorcine pancreatic elastase complexed with beta-casomorphin-7 and Arg-Phe at pH 5.0 (50 min soak)
Components
  • Elastase-1
  • beta-casomorphin-7Casomorphin
KeywordsHYDROLASE / SERINE PROTEINASE
Function / homology
Function and homology information


pancreatic elastase / serine-type endopeptidase activity / proteolysis / extracellular space / metal ion binding
Similarity search - Function
Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases ...Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / Serine proteases, trypsin domain profile. / Serine proteases, trypsin family, serine active site. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
ARGININE / PHENYLALANINE / Chymotrypsin-like elastase family member 1
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsLiu, B. / Schofield, C.J. / Wilmouth, R.C.
Citation
Journal: J.Biol.Chem. / Year: 2006
Title: Structural analyses on intermediates in serine protease catalysis
Authors: Liu, B. / Schofield, C.J. / Wilmouth, R.C.
#1: Journal: Nat.Struct.Biol. / Year: 1997
Title: Structure of a specific acyl-enzyme complex formed between beta-casomorphin-7 and porcine pancreatic elastase
Authors: Wilmouth, R.C. / Clifton, I.J. / Robinson, C.V. / Roach, P.L. / Aplin, R.T. / Westwood, N.J. / Hajdu, J. / Schofield, C.J.
#2: Journal: Nat.Struct.Biol. / Year: 2001
Title: X-ray snapshots of serine protease catalysis reveal a tetrahedral intermediate
Authors: Wilmouth, R.C. / Edman, K. / Neutze, R. / Wright, P.A. / Clifton, I.J. / Schneider, T.R. / Schofield, C.J. / Hajdu, J.
History
DepositionOct 20, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 30, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
P: beta-casomorphin-7
A: Elastase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,2696
Polymers26,7922
Non-polymers4774
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area580 Å2
ΔGint-27 kcal/mol
Surface area10240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.043, 57.705, 74.357
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein/peptide / Protein , 2 types, 2 molecules PA

#1: Protein/peptide beta-casomorphin-7 / Casomorphin


Mass: 863.995 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide
#2: Protein Elastase-1 /


Mass: 25928.031 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00772, pancreatic elastase

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Non-polymers , 5 types, 132 molecules

#3: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2
#4: Chemical ChemComp-PHE / PHENYLALANINE / Phenylalanine


Type: L-peptide linking / Mass: 165.189 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H11NO2
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsOG SER A 195, C ILE P 7 AND N ARG P 1001 ARE COVALENTLY LINKED WITH C ILE P 7 HAVING TETRAHEDRAL GEOMETRY.
Sequence detailsTHIS CONFLICT IS BASED ON THE REFERENCE 3 IN SEQUENCE DATABASE, P00772 IN SWISS-PROT.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2 Å3/Da / Density % sol: 38.59 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN, VAPOR ...Details: 25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2 MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 50 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 127 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 2, 2005 / Details: OSMIC mirrors
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→19.5 Å / Num. obs: 29030 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.062 / Net I/σ(I): 16.8
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.204 / Mean I/σ(I) obs: 4 / Num. unique all: 4151 / % possible all: 99.5

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT1.7data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3EST

3est


Resolution: 1.6→19.5 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.939 / SU B: 3.191 / SU ML: 0.059 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.091 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.211 1474 5.1 %RANDOM
Rwork0.177 ---
all0.179 29030 --
obs0.179 28990 99.64 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.487 Å2
Baniso -1Baniso -2Baniso -3
1-1.56 Å20 Å20 Å2
2--0.13 Å20 Å2
3----1.68 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1810 0 13 128 1951
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211867
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.9192556
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.775240
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.46524.23178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.20815266
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.79159
X-RAY DIFFRACTIONr_chiral_restr0.1240.2292
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021420
X-RAY DIFFRACTIONr_nbd_refined0.2090.2859
X-RAY DIFFRACTIONr_nbtor_refined0.3120.21302
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2126
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.25
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.228
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.213
X-RAY DIFFRACTIONr_mcbond_it2.16621211
X-RAY DIFFRACTIONr_mcangle_it3.04431921
X-RAY DIFFRACTIONr_scbond_it4.1584759
X-RAY DIFFRACTIONr_scangle_it4.8346635
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.234 113 -
Rwork0.171 1988 -
all-2101 -
obs--99.24 %
Refinement TLS params.Method: refined / Origin x: -4.191 Å / Origin y: 28.152 Å / Origin z: 42.862 Å
111213212223313233
T-0.1448 Å2-0.0018 Å2-0.0043 Å2--0.0896 Å2-0.0122 Å2---0.0044 Å2
L1.0358 °20.0392 °2-0.0663 °2-0.7438 °2-0.1873 °2--1.0854 °2
S-0.007 Å °0.0093 Å °-0.0249 Å °-0.0136 Å °0.0021 Å °-0.0204 Å °0.0661 Å °0.0027 Å °0.0049 Å °
Refinement TLS groupSelection: ALL

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